Starting phenix.real_space_refine on Sat Jun 21 09:07:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3d_34464/06_2025/8h3d_34464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3d_34464/06_2025/8h3d_34464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3d_34464/06_2025/8h3d_34464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3d_34464/06_2025/8h3d_34464.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3d_34464/06_2025/8h3d_34464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3d_34464/06_2025/8h3d_34464.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 15615 2.51 5 N 4038 2.21 5 O 4683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24448 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8005 Classifications: {'peptide': 1023} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 971} Chain breaks: 10 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8142 Classifications: {'peptide': 1041} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8119 Classifications: {'peptide': 1039} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 987} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 42 residue: pdb=" N ASN A 122 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 122 " occ=0.24 residue: pdb=" N GLU A 154 " occ=0.22 ... (7 atoms not shown) pdb=" OE2 GLU A 154 " occ=0.51 residue: pdb=" N PHE A 157 " occ=0.58 ... (9 atoms not shown) pdb=" CZ PHE A 157 " occ=0.16 residue: pdb=" N THR A 167 " occ=0.84 ... (5 atoms not shown) pdb=" CG2 THR A 167 " occ=0.32 residue: pdb=" N GLY A 199 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 199 " occ=0.81 residue: pdb=" N ASP A 215 " occ=0.63 ... (6 atoms not shown) pdb=" OD2 ASP A 215 " occ=0.41 residue: pdb=" N GLY A 219 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 219 " occ=0.85 residue: pdb=" N GLU A 340 " occ=0.18 ... (7 atoms not shown) pdb=" OE2 GLU A 340 " occ=0.39 residue: pdb=" N GLY A 446 " occ=0.84 ... (2 atoms not shown) pdb=" O GLY A 446 " occ=0.59 residue: pdb=" N GLY A 447 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 447 " occ=0.24 residue: pdb=" N THR A 470 " occ=0.63 ... (5 atoms not shown) pdb=" CG2 THR A 470 " occ=0.83 residue: pdb=" N GLY A 502 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 502 " occ=0.40 ... (remaining 30 not shown) Time building chain proxies: 15.13, per 1000 atoms: 0.62 Number of scatterers: 24448 At special positions: 0 Unit cell: (148.78, 151.36, 190.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4683 8.00 N 4038 7.00 C 15615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 3.1 seconds 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 53 sheets defined 19.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.602A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.888A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.440A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.721A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.597A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.614A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 770 removed outlier: 3.671A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 removed outlier: 4.053A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 4.135A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 778 through 783' Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.701A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.911A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 822' Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.634A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 874 removed outlier: 4.178A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.825A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.773A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.786A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.599A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.828A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 960 through 965' Processing helix chain 'A' and resid 988 through 993 removed outlier: 4.039A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1001 through 1019 removed outlier: 3.736A pdb=" N GLN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 3.549A pdb=" N ALA A1025 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.516A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.893A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.541A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 765 Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.953A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 777 through 782' Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.912A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 818 through 823 removed outlier: 3.568A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 818 through 823' Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.741A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 856' Processing helix chain 'B' and resid 876 through 881 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.931A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.590A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 931 Processing helix chain 'B' and resid 932 through 939 removed outlier: 3.949A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 965 removed outlier: 3.965A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 978 through 983 removed outlier: 3.977A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 993 removed outlier: 4.143A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 4.132A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1015 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.691A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.835A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 4.052A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.957A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.808A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.508A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 443 removed outlier: 4.007A pdb=" N SER C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.830A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.708A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 751' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.841A pdb=" N GLN C 755 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 756 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 752 through 757' Processing helix chain 'C' and resid 762 through 770 removed outlier: 4.122A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 781 removed outlier: 3.721A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 822 removed outlier: 4.000A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 817 through 822' Processing helix chain 'C' and resid 822 through 827 removed outlier: 4.125A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 856 removed outlier: 3.968A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 875 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.909A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.802A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 932 Processing helix chain 'C' and resid 933 through 941 removed outlier: 3.996A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 958 removed outlier: 4.436A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 removed outlier: 3.585A pdb=" N LEU C 966 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER C 967 " --> pdb=" O LYS C 964 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 968 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 963 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.977A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1002 removed outlier: 3.769A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1015 removed outlier: 4.016A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1028 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.968A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.798A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.891A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.759A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.241A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.771A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.866A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 193 through 196 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.703A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.608A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.608A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.889A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 539 through 542 Processing sheet with id=AB5, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.615A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.515A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 714 removed outlier: 3.772A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.626A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.603A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.684A pdb=" N VAL A1096 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.637A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.525A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.500A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 13.767A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.997A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.500A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.823A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.899A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.084A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.926A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 542 removed outlier: 3.905A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.521A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.096A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.896A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.681A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.584A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.964A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.133A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.133A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.304A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.705A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.648A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.664A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.066A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.987A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 4.079A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AF5, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.647A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.526A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1076 through 1077 removed outlier: 3.785A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.683A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.20 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4307 1.33 - 1.45: 6907 1.45 - 1.58: 13648 1.58 - 1.71: 1 1.71 - 1.83: 141 Bond restraints: 25004 Sorted by residual: bond pdb=" C PRO A 986 " pdb=" O PRO A 986 " ideal model delta sigma weight residual 1.240 1.198 0.042 1.12e-02 7.97e+03 1.42e+01 bond pdb=" C PRO B 986 " pdb=" O PRO B 986 " ideal model delta sigma weight residual 1.240 1.200 0.041 1.12e-02 7.97e+03 1.31e+01 bond pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.31e+01 bond pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" N VAL A 42 " pdb=" CA VAL A 42 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.22e-02 6.72e+03 8.72e+00 ... (remaining 24999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 33893 3.30 - 6.60: 109 6.60 - 9.90: 8 9.90 - 13.20: 1 13.20 - 16.50: 1 Bond angle restraints: 34012 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 114.64 98.14 16.50 1.52e+00 4.33e-01 1.18e+02 angle pdb=" C TYR A 38 " pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " ideal model delta sigma weight residual 110.08 101.78 8.30 1.15e+00 7.56e-01 5.21e+01 angle pdb=" C PRO B 561 " pdb=" CA PRO B 561 " pdb=" CB PRO B 561 " ideal model delta sigma weight residual 112.21 101.82 10.39 1.56e+00 4.11e-01 4.44e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.58 -7.88 1.22e+00 6.72e-01 4.17e+01 angle pdb=" N ILE C 993 " pdb=" CA ILE C 993 " pdb=" C ILE C 993 " ideal model delta sigma weight residual 112.96 107.81 5.15 1.00e+00 1.00e+00 2.66e+01 ... (remaining 34007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12866 17.96 - 35.93: 1671 35.93 - 53.89: 428 53.89 - 71.86: 63 71.86 - 89.82: 27 Dihedral angle restraints: 15055 sinusoidal: 6026 harmonic: 9029 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 -177.18 -89.82 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.09 75.09 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 18.54 74.46 1 1.00e+01 1.00e-02 7.03e+01 ... (remaining 15052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3815 0.115 - 0.229: 65 0.229 - 0.344: 9 0.344 - 0.459: 1 0.459 - 0.574: 1 Chirality restraints: 3891 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA TYR A 38 " pdb=" N TYR A 38 " pdb=" C TYR A 38 " pdb=" CB TYR A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 3888 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 324 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C GLU A 324 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU A 324 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 325 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " 0.050 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO B 812 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 986 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.031 5.00e-02 4.00e+02 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1146 2.72 - 3.26: 21880 3.26 - 3.81: 34535 3.81 - 4.35: 40041 4.35 - 4.90: 73063 Nonbonded interactions: 170665 Sorted by model distance: nonbonded pdb=" OD2 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 689 " pdb=" N GLN A 690 " model vdw 2.237 3.120 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.240 3.040 ... (remaining 170660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 67 or resid 81 through 175 or resid 186 through \ 263 or resid 265 through 622 or resid 639 through 675 or resid 690 through 829 \ or resid 849 through 1144 or resid 1301 through 1303)) selection = (chain 'B' and (resid 27 through 67 or resid 81 through 161 or resid 167 through \ 175 or resid 186 through 231 or resid 236 through 622 or resid 639 through 675 \ or resid 690 through 1144 or resid 1301 through 1303)) selection = (chain 'C' and (resid 27 through 161 or resid 167 through 175 or resid 186 throu \ gh 209 or resid 215 through 231 or resid 236 through 263 or resid 265 through 67 \ 5 or resid 690 through 1144 or resid 1301 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.79 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 58.330 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 25055 Z= 0.180 Angle : 0.608 16.501 34127 Z= 0.335 Chirality : 0.048 0.574 3891 Planarity : 0.004 0.073 4391 Dihedral : 16.862 89.363 9129 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 0.26 % Allowed : 29.38 % Favored : 70.36 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.14), residues: 3049 helix: -2.95 (0.19), residues: 538 sheet: -0.83 (0.21), residues: 627 loop : -2.33 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS C 49 PHE 0.018 0.001 PHE C 133 TYR 0.023 0.001 TYR A 38 ARG 0.004 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 13) link_NAG-ASN : angle 4.14929 ( 39) hydrogen bonds : bond 0.30633 ( 505) hydrogen bonds : angle 9.18401 ( 1335) SS BOND : bond 0.00255 ( 38) SS BOND : angle 1.16335 ( 76) covalent geometry : bond 0.00358 (25004) covalent geometry : angle 0.59037 (34012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 ASN cc_start: 0.8571 (m-40) cc_final: 0.8257 (m110) outliers start: 7 outliers final: 4 residues processed: 121 average time/residue: 0.3441 time to fit residues: 69.1677 Evaluate side-chains 112 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 392 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 0.3980 chunk 242 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 115 GLN B 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.106075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.069914 restraints weight = 56971.292| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.45 r_work: 0.2933 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2859 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2783 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25055 Z= 0.242 Angle : 0.669 11.481 34127 Z= 0.350 Chirality : 0.049 0.379 3891 Planarity : 0.005 0.059 4391 Dihedral : 6.459 58.350 3600 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.51 % Allowed : 27.20 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.14), residues: 3049 helix: -2.79 (0.19), residues: 555 sheet: -0.84 (0.21), residues: 612 loop : -2.49 (0.12), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 436 HIS 0.006 0.001 HIS C1048 PHE 0.020 0.002 PHE B 55 TYR 0.017 0.002 TYR A1067 ARG 0.004 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 13) link_NAG-ASN : angle 4.10046 ( 39) hydrogen bonds : bond 0.06224 ( 505) hydrogen bonds : angle 6.71829 ( 1335) SS BOND : bond 0.00409 ( 38) SS BOND : angle 1.50599 ( 76) covalent geometry : bond 0.00593 (25004) covalent geometry : angle 0.65199 (34012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 111 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 TYR cc_start: 0.5729 (t80) cc_final: 0.5196 (t80) REVERT: B 552 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8392 (mt) REVERT: B 571 ASP cc_start: 0.8852 (p0) cc_final: 0.8474 (p0) REVERT: C 145 TYR cc_start: 0.2554 (OUTLIER) cc_final: 0.2271 (m-10) REVERT: C 248 TYR cc_start: 0.4504 (OUTLIER) cc_final: 0.3431 (m-80) REVERT: C 347 PHE cc_start: 0.4677 (OUTLIER) cc_final: 0.4391 (m-10) REVERT: C 359 SER cc_start: 0.6146 (OUTLIER) cc_final: 0.5563 (m) outliers start: 122 outliers final: 60 residues processed: 222 average time/residue: 0.2951 time to fit residues: 112.2413 Evaluate side-chains 170 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 105 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 16 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 174 optimal weight: 0.0000 chunk 83 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN B 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068839 restraints weight = 55507.256| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.43 r_work: 0.2920 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2783 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2828 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25055 Z= 0.149 Angle : 0.581 11.319 34127 Z= 0.299 Chirality : 0.046 0.352 3891 Planarity : 0.004 0.059 4391 Dihedral : 6.100 59.658 3596 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.95 % Allowed : 28.20 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.14), residues: 3049 helix: -2.64 (0.19), residues: 551 sheet: -0.72 (0.21), residues: 618 loop : -2.42 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS C 49 PHE 0.018 0.001 PHE C 338 TYR 0.015 0.001 TYR A1067 ARG 0.002 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00797 ( 13) link_NAG-ASN : angle 3.88231 ( 39) hydrogen bonds : bond 0.04756 ( 505) hydrogen bonds : angle 6.10690 ( 1335) SS BOND : bond 0.00330 ( 38) SS BOND : angle 1.16150 ( 76) covalent geometry : bond 0.00363 (25004) covalent geometry : angle 0.56394 (34012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 111 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.4861 (t80) REVERT: B 248 TYR cc_start: 0.5672 (t80) cc_final: 0.5156 (t80) REVERT: B 552 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8293 (mt) REVERT: B 571 ASP cc_start: 0.8817 (p0) cc_final: 0.8408 (p0) REVERT: B 906 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.6663 (t80) REVERT: C 96 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5359 (mp0) REVERT: C 145 TYR cc_start: 0.2606 (OUTLIER) cc_final: 0.2171 (m-10) REVERT: C 248 TYR cc_start: 0.4533 (OUTLIER) cc_final: 0.3604 (m-80) REVERT: C 347 PHE cc_start: 0.4587 (OUTLIER) cc_final: 0.4328 (m-10) outliers start: 107 outliers final: 63 residues processed: 209 average time/residue: 0.2911 time to fit residues: 105.4305 Evaluate side-chains 176 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 106 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 217 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 277 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN B 501 ASN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.067408 restraints weight = 55365.516| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.44 r_work: 0.2898 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2828 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2835 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25055 Z= 0.162 Angle : 0.596 11.086 34127 Z= 0.307 Chirality : 0.047 0.349 3891 Planarity : 0.004 0.061 4391 Dihedral : 5.971 58.767 3594 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.69 % Allowed : 28.20 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.14), residues: 3049 helix: -2.63 (0.19), residues: 559 sheet: -0.64 (0.21), residues: 616 loop : -2.44 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS C 49 PHE 0.021 0.001 PHE C 133 TYR 0.015 0.001 TYR A1067 ARG 0.007 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 13) link_NAG-ASN : angle 3.97935 ( 39) hydrogen bonds : bond 0.04682 ( 505) hydrogen bonds : angle 5.91245 ( 1335) SS BOND : bond 0.00508 ( 38) SS BOND : angle 1.66086 ( 76) covalent geometry : bond 0.00394 (25004) covalent geometry : angle 0.57636 (34012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 109 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.5279 (OUTLIER) cc_final: 0.4980 (t80) REVERT: B 248 TYR cc_start: 0.5726 (t80) cc_final: 0.5277 (t80) REVERT: B 490 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.4958 (m-80) REVERT: B 552 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8299 (mt) REVERT: B 571 ASP cc_start: 0.8787 (p0) cc_final: 0.8351 (p0) REVERT: B 906 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.6773 (t80) REVERT: C 96 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5666 (mp0) REVERT: C 145 TYR cc_start: 0.2588 (OUTLIER) cc_final: 0.2120 (m-10) REVERT: C 248 TYR cc_start: 0.4586 (OUTLIER) cc_final: 0.3556 (m-80) REVERT: C 324 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.4783 (pm20) outliers start: 127 outliers final: 89 residues processed: 223 average time/residue: 0.2886 time to fit residues: 111.6042 Evaluate side-chains 202 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 105 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 4.9990 chunk 305 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 279 optimal weight: 0.0670 chunk 213 optimal weight: 30.0000 chunk 177 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074414 restraints weight = 54232.898| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.41 r_work: 0.2969 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2835 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2829 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 25055 Z= 0.098 Angle : 0.536 11.229 34127 Z= 0.272 Chirality : 0.045 0.360 3891 Planarity : 0.004 0.061 4391 Dihedral : 5.478 56.702 3594 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.44 % Allowed : 29.42 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.14), residues: 3049 helix: -2.37 (0.21), residues: 540 sheet: -0.57 (0.21), residues: 641 loop : -2.30 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.000 HIS C 49 PHE 0.017 0.001 PHE C 338 TYR 0.015 0.001 TYR C 396 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 13) link_NAG-ASN : angle 3.77530 ( 39) hydrogen bonds : bond 0.03297 ( 505) hydrogen bonds : angle 5.46843 ( 1335) SS BOND : bond 0.00396 ( 38) SS BOND : angle 1.41789 ( 76) covalent geometry : bond 0.00236 (25004) covalent geometry : angle 0.51742 (34012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 120 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.5248 (t80) REVERT: A 622 VAL cc_start: 0.7877 (m) cc_final: 0.6549 (t) REVERT: A 811 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7070 (mtmt) REVERT: A 849 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 995 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8040 (mtt-85) REVERT: B 226 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6365 (mp) REVERT: B 248 TYR cc_start: 0.5762 (t80) cc_final: 0.5348 (t80) REVERT: B 552 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8217 (mt) REVERT: B 906 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.6659 (t80) REVERT: C 96 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5782 (mp0) REVERT: C 324 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.4694 (pm20) REVERT: C 675 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: C 1127 ASP cc_start: 0.8839 (t0) cc_final: 0.8334 (t0) outliers start: 93 outliers final: 60 residues processed: 208 average time/residue: 0.2962 time to fit residues: 105.6879 Evaluate side-chains 183 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 113 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 118 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 25 optimal weight: 0.9990 chunk 286 optimal weight: 0.0170 chunk 191 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN B 501 ASN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.113885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073813 restraints weight = 53930.346| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.76 r_work: 0.2948 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2829 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2857 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25055 Z= 0.110 Angle : 0.545 11.020 34127 Z= 0.276 Chirality : 0.045 0.354 3891 Planarity : 0.004 0.061 4391 Dihedral : 5.321 57.369 3593 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.99 % Allowed : 28.94 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.14), residues: 3049 helix: -2.33 (0.21), residues: 546 sheet: -0.41 (0.21), residues: 628 loop : -2.29 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS C 49 PHE 0.024 0.001 PHE C 133 TYR 0.020 0.001 TYR C 495 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00798 ( 13) link_NAG-ASN : angle 3.67186 ( 39) hydrogen bonds : bond 0.03558 ( 505) hydrogen bonds : angle 5.40155 ( 1335) SS BOND : bond 0.00430 ( 38) SS BOND : angle 1.35981 ( 76) covalent geometry : bond 0.00269 (25004) covalent geometry : angle 0.52757 (34012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 118 time to evaluate : 5.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5874 (pp) REVERT: A 329 PHE cc_start: 0.5488 (OUTLIER) cc_final: 0.5200 (t80) REVERT: A 811 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7062 (mtmt) REVERT: A 849 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7678 (mm) REVERT: A 878 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9231 (tt) REVERT: A 995 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7812 (mtt-85) REVERT: B 226 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6452 (mp) REVERT: B 248 TYR cc_start: 0.5683 (t80) cc_final: 0.5441 (t80) REVERT: B 552 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 906 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.6631 (t80) REVERT: C 145 TYR cc_start: 0.2399 (OUTLIER) cc_final: 0.1881 (m-10) REVERT: C 241 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8143 (pp) REVERT: C 248 TYR cc_start: 0.4235 (OUTLIER) cc_final: 0.3244 (m-80) REVERT: C 324 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.4639 (pm20) REVERT: C 1127 ASP cc_start: 0.8873 (t0) cc_final: 0.8350 (t0) outliers start: 108 outliers final: 79 residues processed: 217 average time/residue: 0.3722 time to fit residues: 142.8433 Evaluate side-chains 208 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 116 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 56 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 251 optimal weight: 0.4980 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 280 optimal weight: 0.2980 chunk 177 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN B 501 ASN B 506 GLN C 536 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073305 restraints weight = 53902.564| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.74 r_work: 0.2947 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2857 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2880 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25055 Z= 0.114 Angle : 0.548 11.652 34127 Z= 0.277 Chirality : 0.046 0.483 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.340 57.338 3593 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.25 % Allowed : 28.90 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.14), residues: 3049 helix: -2.31 (0.21), residues: 550 sheet: -0.42 (0.21), residues: 627 loop : -2.29 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.005 0.001 HIS C 49 PHE 0.016 0.001 PHE C 338 TYR 0.018 0.001 TYR C 495 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 13) link_NAG-ASN : angle 3.93850 ( 39) hydrogen bonds : bond 0.03566 ( 505) hydrogen bonds : angle 5.36168 ( 1335) SS BOND : bond 0.00369 ( 38) SS BOND : angle 1.36327 ( 76) covalent geometry : bond 0.00277 (25004) covalent geometry : angle 0.52870 (34012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 119 time to evaluate : 5.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5928 (pp) REVERT: A 329 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.5100 (t80) REVERT: A 517 LEU cc_start: -0.0975 (OUTLIER) cc_final: -0.1239 (mm) REVERT: A 811 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7091 (mtmt) REVERT: A 849 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7681 (mm) REVERT: A 878 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9221 (tt) REVERT: A 995 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7810 (mtt-85) REVERT: B 226 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6473 (mp) REVERT: B 552 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8275 (mt) REVERT: B 906 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.6629 (t80) REVERT: C 96 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5581 (mp0) REVERT: C 145 TYR cc_start: 0.2500 (OUTLIER) cc_final: 0.1940 (m-10) REVERT: C 241 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8141 (pp) REVERT: C 248 TYR cc_start: 0.4211 (OUTLIER) cc_final: 0.3204 (m-80) REVERT: C 324 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.4626 (pm20) REVERT: C 675 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: C 1127 ASP cc_start: 0.8849 (t0) cc_final: 0.8311 (t0) outliers start: 115 outliers final: 84 residues processed: 224 average time/residue: 0.4614 time to fit residues: 183.0998 Evaluate side-chains 218 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 118 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 58 optimal weight: 0.0060 chunk 258 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 448 ASN B 188 ASN B 506 GLN B 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.071758 restraints weight = 53525.507| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.67 r_work: 0.2923 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2880 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2902 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25055 Z= 0.174 Angle : 0.598 13.163 34127 Z= 0.306 Chirality : 0.047 0.340 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.578 58.080 3593 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.55 % Allowed : 28.71 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.14), residues: 3049 helix: -2.49 (0.20), residues: 566 sheet: -0.58 (0.21), residues: 623 loop : -2.36 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS C 49 PHE 0.022 0.001 PHE C 133 TYR 0.019 0.001 TYR C 495 ARG 0.003 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 13) link_NAG-ASN : angle 3.77443 ( 39) hydrogen bonds : bond 0.04576 ( 505) hydrogen bonds : angle 5.60164 ( 1335) SS BOND : bond 0.00422 ( 38) SS BOND : angle 1.56531 ( 76) covalent geometry : bond 0.00426 (25004) covalent geometry : angle 0.58013 (34012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 109 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.5977 (pp) REVERT: A 329 PHE cc_start: 0.5380 (OUTLIER) cc_final: 0.5006 (t80) REVERT: A 517 LEU cc_start: -0.0741 (OUTLIER) cc_final: -0.1014 (mm) REVERT: A 878 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9236 (tt) REVERT: A 995 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: B 226 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6431 (mp) REVERT: B 552 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 571 ASP cc_start: 0.8561 (p0) cc_final: 0.8037 (p0) REVERT: B 906 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.6707 (t80) REVERT: C 96 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5511 (mp0) REVERT: C 145 TYR cc_start: 0.2607 (OUTLIER) cc_final: 0.2019 (m-10) REVERT: C 241 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8199 (pp) REVERT: C 248 TYR cc_start: 0.4278 (OUTLIER) cc_final: 0.3132 (m-80) REVERT: C 324 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.4771 (pm20) REVERT: C 675 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8029 (tm-30) outliers start: 123 outliers final: 95 residues processed: 222 average time/residue: 0.2963 time to fit residues: 113.2110 Evaluate side-chains 218 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 109 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 185 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 231 optimal weight: 0.0670 chunk 238 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 269 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 304 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 448 ASN B 188 ASN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.072737 restraints weight = 53450.850| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.70 r_work: 0.2945 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2934 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25055 Z= 0.120 Angle : 0.554 12.283 34127 Z= 0.281 Chirality : 0.045 0.348 3891 Planarity : 0.004 0.060 4391 Dihedral : 5.361 57.278 3593 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.40 % Allowed : 28.82 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.14), residues: 3049 helix: -2.38 (0.20), residues: 553 sheet: -0.53 (0.21), residues: 630 loop : -2.31 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS C 49 PHE 0.017 0.001 PHE C 338 TYR 0.015 0.001 TYR C 495 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 13) link_NAG-ASN : angle 3.69692 ( 39) hydrogen bonds : bond 0.03646 ( 505) hydrogen bonds : angle 5.36732 ( 1335) SS BOND : bond 0.00419 ( 38) SS BOND : angle 1.37378 ( 76) covalent geometry : bond 0.00292 (25004) covalent geometry : angle 0.53705 (34012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 115 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.5994 (pp) REVERT: A 329 PHE cc_start: 0.5388 (OUTLIER) cc_final: 0.5082 (t80) REVERT: A 849 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (mm) REVERT: A 878 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9218 (tt) REVERT: A 995 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8063 (mtt-85) REVERT: B 226 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6294 (mp) REVERT: B 552 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 906 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.6623 (t80) REVERT: C 96 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5884 (mp0) REVERT: C 145 TYR cc_start: 0.2607 (OUTLIER) cc_final: 0.2023 (m-10) REVERT: C 241 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8256 (pp) REVERT: C 248 TYR cc_start: 0.4155 (OUTLIER) cc_final: 0.3020 (m-80) REVERT: C 324 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.4680 (pm20) REVERT: C 359 SER cc_start: 0.5790 (OUTLIER) cc_final: 0.5050 (m) REVERT: C 388 ASN cc_start: 0.8831 (m-40) cc_final: 0.8543 (m110) REVERT: C 675 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: C 1127 ASP cc_start: 0.8904 (t0) cc_final: 0.8408 (t0) outliers start: 119 outliers final: 92 residues processed: 225 average time/residue: 0.3319 time to fit residues: 130.2002 Evaluate side-chains 220 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 113 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 146 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 188 ASN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.071923 restraints weight = 53312.411| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.35 r_work: 0.2948 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2934 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2937 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25055 Z= 0.134 Angle : 0.573 13.821 34127 Z= 0.290 Chirality : 0.046 0.345 3891 Planarity : 0.004 0.061 4391 Dihedral : 5.374 57.588 3593 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.25 % Allowed : 29.05 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.14), residues: 3049 helix: -2.39 (0.20), residues: 554 sheet: -0.54 (0.21), residues: 629 loop : -2.32 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS C 49 PHE 0.022 0.001 PHE C 133 TYR 0.017 0.001 TYR C 495 ARG 0.008 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 13) link_NAG-ASN : angle 3.66596 ( 39) hydrogen bonds : bond 0.03900 ( 505) hydrogen bonds : angle 5.38716 ( 1335) SS BOND : bond 0.00447 ( 38) SS BOND : angle 1.40643 ( 76) covalent geometry : bond 0.00328 (25004) covalent geometry : angle 0.55597 (34012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 113 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6011 (pp) REVERT: A 329 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.5073 (t80) REVERT: A 849 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7744 (mm) REVERT: A 878 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9214 (tt) REVERT: A 995 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7819 (mtt-85) REVERT: B 226 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6196 (mp) REVERT: B 552 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8295 (mt) REVERT: B 565 PHE cc_start: 0.8694 (m-10) cc_final: 0.8485 (m-10) REVERT: B 906 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.6633 (t80) REVERT: C 96 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5864 (mp0) REVERT: C 241 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8237 (pp) REVERT: C 248 TYR cc_start: 0.4239 (OUTLIER) cc_final: 0.3153 (m-80) REVERT: C 324 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.4749 (pm20) REVERT: C 359 SER cc_start: 0.5910 (OUTLIER) cc_final: 0.5417 (m) REVERT: C 388 ASN cc_start: 0.8842 (m-40) cc_final: 0.8554 (m110) REVERT: C 675 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: C 1127 ASP cc_start: 0.8896 (t0) cc_final: 0.8385 (t0) outliers start: 115 outliers final: 93 residues processed: 220 average time/residue: 0.2801 time to fit residues: 106.5801 Evaluate side-chains 218 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 111 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 208 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 300 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 448 ASN B 188 ASN B 506 GLN B1088 HIS C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069708 restraints weight = 53582.477| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.33 r_work: 0.2904 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2937 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2941 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 25055 Z= 0.244 Angle : 0.672 13.362 34127 Z= 0.346 Chirality : 0.049 0.353 3891 Planarity : 0.005 0.061 4391 Dihedral : 5.901 58.864 3593 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.25 % Allowed : 28.97 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.14), residues: 3049 helix: -2.64 (0.19), residues: 569 sheet: -0.81 (0.21), residues: 644 loop : -2.47 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 104 HIS 0.006 0.001 HIS C1048 PHE 0.021 0.002 PHE A1121 TYR 0.021 0.002 TYR C 495 ARG 0.005 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 13) link_NAG-ASN : angle 3.73687 ( 39) hydrogen bonds : bond 0.05562 ( 505) hydrogen bonds : angle 5.85966 ( 1335) SS BOND : bond 0.00578 ( 38) SS BOND : angle 1.85580 ( 76) covalent geometry : bond 0.00600 (25004) covalent geometry : angle 0.65493 (34012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16546.94 seconds wall clock time: 290 minutes 38.45 seconds (17438.45 seconds total)